Just fyi, don't crank the engine for more that 10 or 15 seconds, with at least 30-45 seconds cool down. Pwc starters cannot handle long cranking sessions.
Is it throwing any codes ?
Recheck the gap on the plugs. Pull one and lay it on the head, crank the engine over and check for a healthy blue spark. Check all the grounds, especially between the battery and engine, but find and check them all for cleanliness and tightness.
Check and make sure the air filter is clean.
Have you done a compression check ? have you had the fuel pressure checked ? How does it idle once it has started ? Any missing, sputtering, or surging ?
Check for any loose, bad, or leaking vacuum lines, or intake gaskets, and make sure the intake manifold bolts are not loose.
If all that is good, I would start thinking about clogged fuel injectors. You can take them out and have them pressure cleaned, and reinstall with new orings.
Could be the fuel filter is getting plugged, pump and/or regulator are failing, or just some water in the fuel. Might try some good water remover and get some Startron in the system. Put a small ( I think it's a 1oz bottle) in the tank, add a gallon or two of 92 octane, start the ski and run it on the hose for 30 seconds. Let the ski sit over night. Start it and run on the hose for 1 minute, and let it sit over night. Startron is a enzyme, and very effective cleaner and fuel treatment. Do not worry about over treating with it using the whole 1oz bottle. If your going to try it, use it first without any other treatments or additives.